[bug#46937] (no subject)

[bug#46937] (no subject)

[Mădălin Ionel Patrașcu]

[bug#46937] [PATCH 1/3] gnu: Add r-rcppthread.

[Mădălin Ionel Patrașcu]

* gnu/packages/cran.scm (r-rcppthread): New variable.
---
 gnu/packages/cran.scm | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 1d574b9768..4ac4b4cae1 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -11,7 +11,7 @@
 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
-;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
@@ -2668,6 +2668,27 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
 @code{citation(\"Rcpp\")} for details on these last two.")
     (license license:gpl2+)))
 
+(define-public r-rcppthread
+  (package
+    (name "r-rcppthread")
+    (version "1.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "RcppThread" version))
+       (sha256
+        (base32
+         "1xfcxrny779kgknlvnc4j02ifprnakndnkhx8bhy50d39vp4hjjl"))))
+    (properties `((upstream-name . "RcppThread")))
+    (build-system r-build-system)
+    (home-page
+     "https://github.com/tnagler/RcppThread")
+    (synopsis "R threading in C++")
+    (description
+     "This package provides a C++11-style thread class and thread pool that can
+safely be interrupted from R.")
+    (license license:expat)))
+
 (define-public r-bindr
   (package
     (name "r-bindr")
-- 
2.30.1

[bug#46937] [PATCH 2/3] gnu: Add r-universalmotif.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-universalmotif): New variable.
---
 gnu/packages/bioconductor.scm | 53 ++++++++++++++++++++++++++++++++++-
 1 file changed, 52 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a4d97fad65..55a9b07509 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
-;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -7435,6 +7435,57 @@ data.  This modified test allows for testing differential expression in qPCR
 data.")
     (license license:gpl2+)))
 
+(define-public r-universalmotif
+  (package
+    (name "r-universalmotif")
+    (version "1.8.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "universalmotif" version))
+       (sha256
+        (base32
+         "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc"))))
+    (properties
+     `((upstream-name . "universalmotif")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-link
+           (lambda _
+             (substitute* "src/Makevars"
+               (("/usr/bin/strip") (which "strip")))
+             #t)))))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggseqlogo" ,r-ggseqlogo)
+       ("r-iranges" ,r-iranges)
+       ("r-mass" ,r-mass)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rcppthread" ,r-rcppthread)
+       ("r-rdpack" ,r-rdpack)
+       ("r-rlang" ,r-rlang)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-yaml" ,r-yaml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page
+     "https://bioconductor.org/packages/universalmotif/")
+    (synopsis
+     "Specific structures importer, modifier, and exporter for R")
+    (description
+     "This package allows importing most common @dfn{specific structure}
+(motif) types into R for use by functions provided by other Bioconductor
+motif-related packages.  Motifs can be exported into most major motif formats
+from various classes as defined by other Bioconductor packages.  A suite of
+motif and sequence manipulation and analysis functions are included, including
+enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
+motifs, and others.")
+    (license license:gpl3)))
+
 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
 ;; it here.
 (define-public r-activedriverwgs
-- 
2.30.1

[bug#46937] [PATCH 3/3] gnu: Add r-circrnaprofiler.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-circrnaprofiler): New variable.
---
 gnu/packages/bioconductor.scm | 53 +++++++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 55a9b07509..2da2be6ae3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6810,6 +6810,59 @@ accessibility data.")
          ,@(alist-delete "r-monocle"
                          (package-propagated-inputs r-cicero)))))))
 
+(define-public r-circrnaprofiler
+  (package
+    (name "r-circrnaprofiler")
+    (version "1.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "circRNAprofiler" version))
+       (sha256
+        (base32
+         "1rwpl9a5p5242aiapik0vf4ywqh7m6phzl8z8qmzcy0imbx7mpbn"))))
+    (properties
+     `((upstream-name . "circRNAprofiler")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationhub" ,r-annotationhub)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+       ("r-deseq2" ,r-deseq2)
+       ("r-dplyr" ,r-dplyr)
+       ("r-edger" ,r-edger)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gwascat" ,r-gwascat)
+       ("r-iranges" ,r-iranges)
+       ("r-magrittr" ,r-magrittr)
+       ("r-r-utils" ,r-r-utils)
+       ("r-readr" ,r-readr)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rlang" ,r-rlang)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-seqinr" ,r-seqinr)
+       ("r-stringi" ,r-stringi)
+       ("r-stringr" ,r-stringr)
+       ("r-universalmotif" ,r-universalmotif)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page
+     "https://github.com/Aufiero/circRNAprofiler")
+    (synopsis
+     "Computational framework for the downstream analysis of circular RNA's")
+    (description
+     "@code{r-circrnaprofiler} is a computational framework for a comprehensive
+in silico analysis of @dfn{circular RNA} (circRNAs).  This computational
+framework allows to combine and analyze circRNAs previously detected by
+multiple publicly available annotation-based circRNA detection tools.  It
+covers different aspects of circRNAs analysis from differential expression
+analysis, evolutionary conservation, biogenesis to functional analysis.")
+    (license license:gpl3)))
+
 (define-public r-cistopic
   (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
         (revision "0"))
-- 
2.30.1

bug#46937: [PATCH 1/3] gnu: Add r-rcppthread.

[Ricardo Wurmus]

Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

> * gnu/packages/cran.scm (r-rcppthread): New variable. […]
> * gnu/packages/bioconductor.scm (r-universalmotif): New variable. […]
> * gnu/packages/bioconductor.scm (r-circrnaprofiler): New variable.

Applied with minor changes: we no longer end phases with #t.

Thank you!

-- 
Ricardo